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Commits on Jul 28, 2013

• Made a general-purpose public method

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Commits on Mar 2, 2013

• get pariwise alignment of protein sequences

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  andreasprlic

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Commits on Nov 28, 2012

• adding another database type constant

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  aalhossary

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Commits on Nov 27, 2012

• Proper fixation of the bug, adding INFINITY as a constant, and documentation

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Commits on Nov 26, 2012

• correcting a bug that takes place at the end of the file (if you reach it ;) )

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  aalhossary

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Commits on Nov 24, 2012

• just doc

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  aalhossary

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Commits on Nov 19, 2012

• Changing return of parse() into List in stead of Vector

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  aalhossary

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• Adding getBioSequences(boolean ignoreCase)

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  aalhossary

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Commits on Nov 9, 2012

• Replacing System.lineSeparator() calls with the backwards-compatible getProperty("line.separator")

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  sbliven

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Commits on Nov 7, 2012

• Changing parseFile(xxx) function set into parse(xxx) and adding parseNext(int)

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  aalhossary

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Commits on Nov 6, 2012

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• Added Stockholm Parser beta, and some test files.

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  aalhossary

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Commits on Oct 18, 2012

• Refactor to use forester 1.005

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  markchapman

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Commits on Jul 3, 2012

• demo for how to load amino acid substitution matrices

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  andreasprlic

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• an example for how to align DNA

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  andreasprlic

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• adding the cookbook example as a demo

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  andreasprlic

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Commits on Jul 2, 2012

• adding patch by Don Naki

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  andreasprlic

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Commits on Mar 8, 2012

• added sanity check to Alignments, throws IllegalArgumentException if compound sets mismatch (instead of just failing silently)

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  brandstaetter

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Commits on Jan 10, 2012

• fixing recursion

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  andreasprlic

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Commits on Oct 8, 2011

• Minor documentation changes

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  sbliven

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Commits on Aug 3, 2011

• fixing patch provided by Tariq

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  andreasprlic

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Commits on Jul 6, 2011

• Contributing new framework for loading amino acid substitution matrices from the AAINDEX database.

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  andreasprlic

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Commits on Jan 31, 2011

• making access methods public

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  andreasprlic

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Commits on Nov 23, 2010

• common code moved to IOUtils in core

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  markchapman

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Commits on Nov 19, 2010

• update to latest drawing code

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  andreasprlic

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• fix compiler warnings

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  markchapman

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• fix CruiseControl javadoc warnings

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  markchapman

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• refactoring to integrate anchored and standard alignment

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  markchapman

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Commits on Nov 3, 2010

• Sequence.getReverse() has been changed to getInverse() to avoid confusion.

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  andrewyatz

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Commits on Nov 2, 2010

• Modified in line with latest version of biojava3-core's Sequence interface

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  andrewyatz

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Commits on Oct 21, 2010

• now with nicer web display

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  andreasprlic

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Commits on Sep 28, 2010

• fixing a junit test

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  andreasprlic

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• now conservation also works with Accession IDs

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  andreasprlic

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• adding new StringFormat

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  andreasprlic

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• adding display of sequence conservation for pairwise alignments

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  andreasprlic

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